3-1798009-G-A

Variant names:

• chr3-1798009-G-A
• rs10510217

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.141 in 152,122 control chromosomes in the GnomAD database, including 1,796 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1796 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21478 AN: 152004 Hom.: 1789 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0652

Gnomad FIN AF: 0.0628

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.139

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.141 AC: 21493 AN: 152122 Hom.: 1796 Cov.: 32 AF XY: 0.135 AC XY: 10031 AN XY: 74390

African (AFR) AF: 0.207 AC: 8602 AN: 41478

American (AMR) AF: 0.124 AC: 1891 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3470

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.0655 AC: 316 AN: 4826

European-Finnish (FIN) AF: 0.0628 AC: 666 AN: 10602

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9105 AN: 67976

Other (OTH) AF: 0.137 AC: 290 AN: 2114

Alfa AF: 0.135 Hom.: 3120

Bravo AF: 0.152

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.72
PhyloP100		0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10510217; hg19: chr3-1839693;